Genomic inbreeding measures applied to a population of mice divergently selected for birth weight environmental variance

Abstract

This study aimed to compare different inbreeding measures estimated from pedigree and molecular data from two divergent mouse lines selected for environmental birth weight during 26 generations. Furthermore, the performance of different approaches and both molecular and pedigree data sources for estimating Ne were tested in this population. A total of 1,699 individuals were genotyped using a high-density genotyping array. Genomic relationship matrices were used to calculate molecular inbreeding: Nejati-Javaremi (F _NEJ), Li and Horvitz (F _L&H), Van Raden method 1 (F _VR1) and method 2 (F _VR2), and Yang (F _YAN). Inbreeding based on runs of homozygosity (F _ROH) and pedigree inbreeding (F _PED) were also computed. F _ROH, F _NEJ, and F _L&H were also adjusted for their average values in the first generation of selection and named F _ROH0, F _NEJ0, and F _L&H0. ∆F was calculated from pedigrees as the individual inbreeding rate between the individual and his parents (∆F _PEDt) and individual increases in inbreeding (∆F _PEDi). Moreover, individual ∆F was calculated from the different molecular inbreeding coefficients (∆F _NEJ0, ∆F _L&H, ∆F _L&H0, ∆F _VR1, ∆F _VR2, ∆F _YAN, and ∆F _ROH0). The Ne was obtained from different ∆F, such as Ne _PEDt, Ne _PEDi, Ne _NEJ0, Ne _L&H, Ne _L&H0, Ne _VR1, Ne _VR2, Ne _YAN, and Ne _ROH0. Comparing with F _PED , F _ROH , F _NEJ and F _VR2 overestimated inbreeding while F _NEJ0 , F _L&H , F _L&H0 , F _VR1 and F _YAN underestimated inbreeding. Correlations between inbreeding coefficients and ∆F were calculated. F _ROH had the highest correlation with F _PED (0.89); F _YAN had correlations >0.95 with all the other molecular inbreeding coefficients. Ne _PEDi was more reliable than Ne _PEDt and presented similar behaviour to Ne _L&H0 and Ne _NEJ0. Stable trends in Ne were not observed until the 10th generation. In the 10th generation Ne _PEDi was 42.20, Ne _L&H0 was 45.04 and Ne _NEJ0 was 45.05 and in the last generation these Ne were 35.65, 35.94 and 35.93, respectively F _ROH presented the highest correlation with F _PED, which addresses the identity by descent probability (IBD). The evolution of Ne _L&H0 and Ne _NEJ0 was the most similar to that of Ne _PEDi. Data from several generations was necessary to reach a stable trend for Ne, both with pedigree and molecular data. This population was useful to test different approaches to computing inbreeding coefficients and Ne using molecular and pedigree data.

Keywords: birth weight environmental variability; divergent selection; effective population size; genomic inbreeding; increase in inbreeding.